A major aim of the Integrative Immunobiology Unit is to decipher gene expression programs that direct cell fates in the hematopoietic and immune system. We seek knowledge that will provide insights for understanding immunodeficiencies, autoimmunities and effective immune responses. For a tractable model system to prototype our approaches, we are taking advantage of CD4+ T helper cell differentiation since many research tools are available for this system and much is already known about its core transcriptional program and signaling pathways. However, relatively little is known about post-transcriptional control of gene expression and the roles of non-coding RNAs in this context. The focus of this project is a class of endogenous small untranslated RNAs called microRNAs (miRNAs) that partner with Argonaute (Ago) proteins to form effector RNA-induced silencing complexes (RISCs) that recognize cognate mRNA targets and reduce their stability. It became evident that miRNAs are required for B and T lymphocyte differentiation when miRNA biogenesis was blocked by conditional ablation of the processing enzyme Dicer in a genetically engineered mouse model. Previously, we successfully combined mouse genetics and genomics to systematically determine the impact of miRNAs on the transcriptome. We will continue with this approach to integrate miRNAs into maps of regulatory networks that orchestrate gene expression in lymphocytes. To accomplish our goals we are establishing state-of-the-art genomic methods enabled by massively parallel sequencing.